SMTL ID : 7dl4.1

Crystal structure of human serum albumin and nitrosylruthenium complex adduct

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

2 x RU: RUTHENIUM ION(Non-covalent)(Non-functional Binders)

RU.1: 6 residues within 4Å: Chain A: H.146 Ligands: HZQ.2, CL.3, CL.4, CL.5, NO.6 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: NO.6 RU.7: 5 residues within 4Å: Ligands: GOL.8, CL.9, CL.10, CL.11, NO.12 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: NO.12

1 x HZQ: 5-chloranylquinolin-8-ol(Non-covalent)

HZQ.2: 12 residues within 4Å: Chain A: I.142, H.146, F.149, F.157, Y.161, G.189, K.190 Ligands: RU.1, CL.3, CL.4, CL.5, NO.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.142, A:I.142, A:F.149

7 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 5 residues within 4Å: Chain A: H.146 Ligands: RU.1, HZQ.2, CL.4, NO.6 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Ligands: RU.1, HZQ.2, CL.3, CL.5, NO.6 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain A: K.190 Ligands: RU.1, HZQ.2, CL.4, NO.6 Ligand excluded by PLIP CL.9: 7 residues within 4Å: Chain A: F.134, K.137 Ligands: RU.7, GOL.8, CL.10, CL.11, NO.12 Ligand excluded by PLIP CL.10: 7 residues within 4Å: Chain A: K.137, Y.138, E.141 Ligands: RU.7, GOL.8, CL.9, CL.11 Ligand excluded by PLIP CL.11: 6 residues within 4Å: Chain A: K.137 Ligands: RU.7, GOL.8, CL.9, CL.10, NO.12 Ligand excluded by PLIP CL.22: 1 residues within 4Å: Ligands: GOL.8 Ligand excluded by PLIP

2 x NO: NITRIC OXIDE(Non-covalent)

NO.6: 6 residues within 4Å: Chain A: H.146 Ligands: RU.1, HZQ.2, CL.3, CL.4, CL.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.146 NO.12: 5 residues within 4Å: Chain A: P.118 Ligands: RU.7, GOL.8, CL.9, CL.11 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 9 residues within 4Å: Chain A: P.118, F.134, Y.138 Ligands: RU.7, CL.9, CL.10, CL.11, NO.12, CL.22 No protein-ligand interaction detected (PLIP) GOL.14: 5 residues within 4Å: Chain A: K.199, S.202, F.211, W.214, L.481 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.199, A:S.202 Water bridges: A:K.199, A:S.202, A:F.211 GOL.15: 4 residues within 4Å: Chain A: L.219, R.222, L.238, H.242 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.222 GOL.16: 8 residues within 4Å: Chain A: Y.30, H.67, F.70, N.99, G.248, D.249, L.250, L.251 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.248, A:D.249, A:L.250, A:L.251 Water bridges: A:K.106

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.13: 9 residues within 4Å: Chain A: K.106, Y.148, Y.150, A.151, C.245, G.248, D.249, L.250, C.253 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.106

5 x PLM: PALMITIC ACID(Non-covalent)

PLM.17: 15 residues within 4Å: Chain A: R.10, L.22, V.46, L.66, F.70, Y.150, P.152, L.250, L.251, A.254, R.257, A.258, L.283, L.284, S.287 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.22, A:V.46, A:L.66, A:F.70, A:F.70, A:P.152, A:L.250, A:L.251, A:A.254, A:L.283 Hydrogen bonds: A:S.287 Water bridges: A:S.287, A:S.287 Salt bridges: A:R.257 PLM.18: 14 residues within 4Å: Chain A: S.342, V.344, R.348, L.387, I.388, N.391, F.403, Y.411, L.430, C.438, A.449, L.453, R.485 Ligands: PLM.20 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.387, A:I.388, A:F.403, A:L.430, A:L.430, A:A.449, A:L.453 Hydrogen bonds: A:S.342 Salt bridges: A:R.348, A:R.485 PLM.19: 10 residues within 4Å: Chain A: R.209, A.210, A.213, F.228, S.232, D.324, G.328, L.347, K.351, E.354 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.228, A:L.347, A:K.351, A:K.351 Salt bridges: A:K.351 PLM.20: 13 residues within 4Å: Chain A: L.387, R.410, Y.411, K.414, V.418, L.430, L.457, L.460, H.464, R.485, F.488, S.489 Ligands: PLM.18 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.411, A:Y.411, A:Y.411, A:V.418, A:L.430, A:L.457, A:L.460, A:H.464, A:F.488, A:F.488 Hydrogen bonds: A:Y.411, A:Y.411 Salt bridges: A:R.410, A:K.414 PLM.21: 13 residues within 4Å: Chain A: Y.401, N.405, F.502, F.507, K.525, A.528, L.529, L.532, M.548, F.551, V.576, S.579, Q.580 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.502, A:F.507, A:F.507, A:K.525, A:L.529, A:L.532, A:L.532, A:M.548, A:F.551, A:F.551, A:Q.580 Hydrogen bonds: A:N.405 Salt bridges: A:K.402, A:K.525

Links

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Citation

Xie, L.L. et al., Structural and Photodynamic Studies on Nitrosylruthenium Complexed Serum Albumin. To Be Published

Release Date

2021-12-01

Peptides

Serum albumin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Serum albumin

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